pawan raghav wrote:
Dear Justin,
No dear I have not modelled the membrane, my protein is a simple protein
which contained a loop about 59 amino acids. So I am intrested to model
this loop through MD simulation. In this concerned I did 15 ns
simulations, but right now don't know how to perform sampling for my
protein (which is not a membrane, thermophilic or mesophilic protein) on
same temperature i.e. 300k. In this regard is it correct to perform
REMD, if yes then tell me how to perform it on single CPU? I am asking
from you again to sure I can perform ot is it right to use REMD in my
protein condition which in not a thermophilic protein. I think that REMD
can only apply to those proteins which are thermophilic or mesophilic.
please comment on this.
REMD has nothing to do with whether or not the protein is thermophilic. Please
do some background reading on the technique. You need multiple processors to
run the simulation. The different replicates must be run concurrently so that
they may periodically exchange.
Since you are not modeling a membrane, I again wonder how you settled on the
force field you did. Not that I think there's anything wrong with 53A6 (except
for a bias towards extended structures, which you would have discovered with a
bit of background reading). Just be prepared to justify your choice to a
critical audience...
Yes I wanted to sample loop dynamics, for which you have mentioned
to run several simulations at the relevant (physiological?) temperature.
Is it mean to run several (2,3,4..etc) diferent simulations at different
time steps like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results
to obtain some averages from each and every simulations but it gives
several averages values then how to sample all these simulations and
finally how to get the average from these simulations.
My suggestion was to run several simulations of equivalent length (such that the
properties of interest converge) and obtain averages not only along each
simulation, but also among all of them.
-Justin
--
Pawan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
